What is the minimum coverage adequate for variant calls from Whole Genome Sequencing data?
2
2
Entering edit mode
5.0 years ago

This is a question from my collaborator. He has not sent his samples to do the whole genome sequencing yet. Does anyone know the minimum coverage that is necessary for reliable variant calls from Whole Genome Sequencing data?

Thank you so much.

next-gen Whole Geneome Seq coverage • 3.6k views
ADD COMMENT
2
Entering edit mode
5.0 years ago
Paul ★ 1.4k

In case you are calling germline variants - this is interesting article. Basically it is very hard to answer your question. Probably in exome sequencing it could be between 30x-50x. For WGS see this and this interesting article.

ADD COMMENT
1
Entering edit mode
5.0 years ago
apa@stowers ▴ 540

Ditto what Paul said.

Organism, experimental design and algorithm may also have big effects. Some variant callers (like GATK) make it possible to leverage information across samples, increasing effective depth. Depending on what you're doing, you could also consider RNAseq, which will drastically increase coverage given the same number of reads, but you only see the genes...

If you are looking for causal variants, I have seen some approaches which have succeeded with < 10x depth, but these were in Danio, using large embryo pools, which boosts apparent heterozygosity and makes detecting homozygous regions easier (for instance SNPTrack).

ADD COMMENT

Login before adding your answer.

Traffic: 2476 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6